Adaptation of A-to-I RNA editing in Drosophila

Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing

(2017) Rui Zhang et al.   PLoS Genetics

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data

(2016) Melanie Schirmer et al.   BMC BIOINFORMATICS

Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications

(2016) Konstantin Licht et al.   JOURNAL OF CELL BIOLOGY

The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection

(2016) Yao Yu et al.   PLoS Genetics

Dynamic response of RNA editing to temperature in Drosophila

(2015) Leila E Rieder et al.   BMC BIOLOGY

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

(2015) David Laehnemann et al.   BRIEFINGS IN BIOINFORMATICS

Determinants of the rate of protein sequence evolution

(2015) Jianzhi Zhang et al.   NATURE REVIEWS GENETICS

Genetic Determinants of RNA Editing Levels of ADAR Targets in Drosophila melanogaster

(2015) Yerbol Z. Kurmangaliyev et al.   G3-Genes Genomes Genetics

Global Diversity Lines–A Five-Continent Reference Panel of Sequenced Drosophila melanogaster Strains

(2015) Jennifer K. Grenier et al.   G3-Genes Genomes Genetics

The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing

(2015) Shahar Alon et al.   eLife

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Profiling the RNA editomes of wild-typeC. elegansand ADAR mutants

(2014) Han-Qing Zhao et al.   GENOME RESEARCH

A biochemical landscape of A-to-I RNA editing in the human brain transcriptome

(2014) M. Sakurai et al.   GENOME RESEARCH

Estimating genotype error rates from high-coverage next-generation sequence data

(2014) Jeffrey D. Wall et al.   GENOME RESEARCH

In Search of Beneficial Coding RNA Editing

(2014) Guixia Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Robustly detecting differential expression in RNA sequencing data using observation weights

(2014) Xiaobei Zhou et al.   NUCLEIC ACIDS RESEARCH

Human coding RNA editing is generally nonadaptive

(2014) G. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Editome in Rhesus Macaque Shaped by Purifying Selection

(2014) Jia-Yu Chen et al.   PLoS Genetics

Identification of evolutionarily meaningful information within the mammalian RNA editing landscape

(2014) Yiannis A Savva et al.   GENOME BIOLOGY

Mammalian conserved ADAR targets comprise only a small fragment of the human editosome

(2014) Yishay Pinto et al.   GENOME BIOLOGY

How epigenetic mutations can affect genetic evolution: Model and mechanism

(2013) Filippos D. Klironomos et al.   BIOESSAYS

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes

(2013) L. Bazak et al.   GENOME RESEARCH

Reduction of RNA A-to-I editing in Drosophila acclimated to heat shock

(2013) Joel Stocker et al.   KAOHSIUNG JOURNAL OF MEDICAL SCIENCES

PAMLX: A Graphical User Interface for PAML

(2013) B. Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identifying RNA editing sites using RNA sequencing data alone

(2013) Gokul Ramaswami et al.   NATURE METHODS

Deciphering the functions and regulation of brain-enriched A-to-I RNA editing

(2013) Jin Billy Li et al.   NATURE NEUROSCIENCE

Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila

(2013) Georges St Laurent et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RADAR: a rigorously annotated database of A-to-I RNA editing

(2013) Gokul Ramaswami et al.   NUCLEIC ACIDS RESEARCH

Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly

(2013) C. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Systematic identification of edited microRNAs in the human brain

(2012) S. Alon et al.   GENOME RESEARCH

Adar is essential for optimal presynaptic function

(2012) Carolina Maldonado et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

Nascent-Seq Indicates Widespread Cotranscriptional RNA Editing in Drosophila

(2012) Joseph Rodriguez et al.   MOLECULAR CELL

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

(2012) J.-R. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses

(2012) S. Garrett et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) J. K. Pickrell et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) W. Lin et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) C. L. Kleinman et al.   SCIENCE

Auto-regulatory RNA editing fine-tunes mRNA re-coding and complex behaviour in Drosophila

(2012) Yiannis A. Savva et al.   Nature Communications

The Genomic Landscape and Evolutionary Resolution of Antagonistic Pleiotropy in Yeast

(2012) Wenfeng Qian et al.   Cell Reports

The ADAR protein family

(2012) Yiannis A Savva et al.   GENOME BIOLOGY

High levels of RNA-editing site conservation amongst 15 laboratory mouse strains

(2012) Petr Daneck et al.   GENOME BIOLOGY

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Very Few RNA and DNA Sequence Differences in the Human Transcriptome

(2011) Daniel R. Schrider et al.   PLoS One

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

(2011) M. Li et al.   SCIENCE

A-to-I RNA Editing is Induced Upon Hypoxia

(2011) Yael Nevo-Caspi et al.   SHOCK

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats

(2010) Yoav Kleinberger et al.   BMC GENOMICS

One Hundred Years of Pleiotropy: A Retrospective

(2010) F. W. Stearns   GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Engineered Alterations in RNA Editing Modulate Complex Behavior inDrosophila

(2010) James E. C. Jepson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Heat Shock Response: Life on the Verge of Death

(2010) Klaus Richter et al.   MOLECULAR CELL

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Rate, molecular spectrum, and consequences of human mutation

(2010) M. Lynch   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

RNA editing: a driving force for adaptive evolution?

(2009) Willemijn M. Gommans et al.   BIOESSAYS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Large-scale mRNA sequencing determines global regulation of RNA editing during brain development

(2009) H. Wahlstedt et al.   GENOME RESEARCH

Adenosine deamination in human transcripts generates novel microRNA binding sites

(2009) Glen M. Borchert et al.   HUMAN MOLECULAR GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

(2009) J. B. Li et al.   SCIENCE

Adenosine-to-inosine RNA editing

(2009) Boris Zinshteyn et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA editing in regulating gene expression in the brain

(2007) James E.C. Jepson et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms